Index: trunk/MagicSoft/Mars/Changelog
===================================================================
--- trunk/MagicSoft/Mars/Changelog	(revision 8005)
+++ trunk/MagicSoft/Mars/Changelog	(revision 8006)
@@ -18,4 +18,15 @@
 
                                                  -*-*- END OF LINE -*-*-
+
+ 2006/10/06 Daniela Dorner
+
+   * scripts/processsequence:
+     - implemented command line options
+     - improved logging
+     - implemented checks
+     - removed sourcefile
+
+
+
  2006/10/05 Stefan Ruegamer
 
Index: trunk/MagicSoft/Mars/scripts/processsequence
===================================================================
--- trunk/MagicSoft/Mars/scripts/processsequence	(revision 8005)
+++ trunk/MagicSoft/Mars/scripts/processsequence	(revision 8006)
@@ -18,7 +18,7 @@
 #
 #
-#   Author(s): Daniela Dorner  08/2004 <mailto:dorner@astro.uni-wuerzburg.de>
-#
-#   Copyright: MAGIC Software Development, 2000-2004
+#   Author(s): Daniela Dorner  10/2006 <mailto:dorner@astro.uni-wuerzburg.de>
+#
+#   Copyright: MAGIC Software Development, 2000-2006
 #
 #
@@ -40,117 +40,281 @@
 ##############################################################################
 
-#function to create directory
-function makedir()
+#to be set by the user (if you don't use the command-line options)
+#path of your output directory
+#outpath=/home/dorner/ToO
+outpath=
+#give either sequence number or sequence file (including path)
+sequence=
+sequfile=""
+
+function usage()
 {
-   if [ ! -d $@ ]
+   echo "Usage: $0 [options]"
+   echo "options:"
+   echo -n "  --sequ sequence#       "
+   echo " giving number of sequence which shall be processed "
+   echo -n "  --sequ-file sequfile   "
+   echo " giving sequencfile (including path) of sequence which shall be processed "
+   echo -n "  --out outpath          "
+   echo " giving the path where all outputfiles are stored "
+   echo -n "  -cal                   "
+   echo " running only calibration"
+   echo -n "  -b                     "
+   echo " running in non-interactive mode (i.e. you are not asked if the paths are ok)"
+#   echo -n "  -merppu                "
+#   echo " running only merppupdate"
+   echo -n "  -star                  "
+   echo " running only star"
+   echo ""
+   echo "Remarks: "
+   echo    " - you can set the variables (or part of it) also in the script "
+   echo    " - you have to set the outpath and either the sequence number or the sequence file"
+   echo    "    (if both is set, the sequence given by the sequencefile is processed)"
+   echo "" 
+   exit
+}
+
+interactive="yes"
+
+while [ "$1" ]
+do 
+   case $1 in 
+           --sequ)  shift
+                    sequence=$1
+                    ;;
+           --mars)  shift
+                    mars=$1
+                    ;;
+            --out)  shift
+                    outpath=$1
+                    ;;
+               -b)  interactive='no'
+                    ;;
+             -cal)  cal='yes'
+                    ;;
+#          -merppu)  merppu='yes'
+#                    ;;
+            -star)  star='yes'
+                    ;;
+      --sequ-file)  shift
+                    sequfile=$1
+                    ;;
+               -h)  usage
+                    ;;
+      *)      echo "unknown option $1 "
+              usage
+              exit
+              ;;
+   esac
+   shift
+done
+
+##getting settings for root
+#if [ "$mars" = "" ]
+#then
+#   echo "WARNING Mars-Version has not been set"
+#   echo ""
+#   usage
+#fi
+#source $mars/datacenter/scripts/setup
+
+if [ "$outpath" = "" ]
+then
+   echo "WARNING outpath has not been set"
+   echo ""
+   usage
+fi
+
+if [ "$sequence" = "" ] && [ "$sequfile" = "" ]
+then
+   echo "WARNING neither sequ nor sequfile has been set"
+   echo ""
+   usage
+fi
+
+echo ""
+echo "You have set the variables to: "
+#echo "mars:     "$mars
+echo " outpath:  "$outpath
+
+if [ "$sequfile" = "" ]
+then 
+   if ! n8=`printf %08d $sequence`
    then
-     mkdir -pv $@ 
-     if [ ! -d $@ ]
-     then 
-        echo "could not make dir "$@
-        exit
-     fi
-   fi
-}
-
-
-#to be set by the user 
-mars=/home/user/Mars
-outpath=/home/user/outpath
-sequence=55221
-
-
-#needed if not set in .bashrc or when script is e.g. executed in cronjob
-export ROOTSYS=/opt/root_v4.04.02g
-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROOTSYS/lib
-export PATH=$PATH:$ROOTSYS/bin
-
-
-no=`printf %08d $sequence | cut -c 1-4`
-sequfile="/magic/sequences/"$no"/sequence"`printf %08d $sequence`".txt"
-calpath=$outpath"/callisto/"`printf %08d $sequence`
-starpath=$outpath"/star/"`printf %08d $sequence`
-
-echo "mars:     "$mars
-echo "outpath:  "$outpath
-echo "sequence: "$sequence
-echo "sequfile: "$sequfile
-echo "path where calibration files are stored : "$calpath
-echo "path where star files are stored        : "$starpath
-
-makedir $calpath
-makedir $starpath
-
-cd $mars
-
-echo "run callisto..."
-echo "./callisto -b -q -f --log=$calpath/callisto$sequence.log --out=$calpath $sequfile "
-./callisto -b -q -f --log=$calpath/callisto$sequence.log --out=$calpath $sequfile 
-echo "callisto is finished "
-echo ""
-
-
-
-calfiles=`find $calpath -name [2][0][0-2][0-9][0,1][0-9][0-3][0-9]_*_Y_*.root`
-
-echo "run merpp update for calibrated files..."
-echo "calibrated data files: "$calfiles
-
-for calfile in ${calfiles[@]}
-do 
-   echo "calfile: "$calfile 
-   outpath=`dirname $calfile`
-   echo "outpath: "$outpath
-   
-   merpplogpath=$outpath"/merpplogs"
-   makedir $merpplogpath
-   
-   runno=`echo $calfile | cut -d_ -f2 | sed -e 's/^0//' | sed -e 's/^0//' | sed -e 's/^0//' `
-   ccfile=`find /magic/subsystemdata/cc/ -name [2][0][0-2][0-9][0,1][0-9][0-3][0-9]_*${runno}_[P,D,C,S]_*_S.rep`
-   cacofile=`find /magic/subsystemdata/caco/ -name dc_[2][0][0-2][0-9]_[0,1][0-9]_[0-3][0-9]_*${runno}_*.txt`
-   echo "runno: "$runno 
-   echo "ccfile: "$ccfile 
-   if [ "$ccfile" = "" ]
-   then
-      echo "no ccfile found for run "$runno 
-      break
-   fi
-   echo "cacofile: "$cacofile 
-   if [ "$cacofile" = "" ]
-   then 
-      echo "no cacofile found for run "$runno 
-      echo "finding cacofile..." 
-      for (( i = 0; i <= 10; i++ ))
-      do 
-         newrun=`echo $runno - $i | bc`
-  #      echo "$missingcacorun + $i = $newrun"
-         path=`dirname $ccfile`
-         path=`echo $path | sed -e 's/cc/caco/'`
-         echo "path: "$path 
-         cacofile=`find $path -name *$newrun*`
-         if [ "$cacofile" = "" ]
-         then
-            continue
-         else
-            break
-            echo "cacofile: "$cacofile 
-         fi
-      done
-   fi
-   echo "./merpp -u --log=$merpplogpath/merppccupdate$runno.log --runfile=$runno $ccfile $calfile "
-   ./merpp -u --log=$merpplogpath/merppccupdate$runno.log --runfile=$runno $ccfile $calfile 
-
-   echo "./merpp -u --log=$merpplogpath/merppcacoupdate$runno.log --auto-time $cacofile $calfile "
-   ./merpp -u --log=$merpplogpath/merppcacoupdate$runno.log --auto-time $cacofile $calfile 
-done
-echo "merppupdate is finished"
-echo ""
-
-
-
-echo "run star..."
-echo "./star -b -q -f --log=$starpath/star$sequence.log --ind=$callistopath --out=$starpath $sequfile "
-./star -b -q -f --log=$starpath/star$sequence.log --ind=$callistopath --out=$starpath $sequfile 
-echo "star is finished "
-
-
+      echo "your sequence number is not valid"
+      usage
+      exit
+   fi
+   no=`echo $n8 | cut -c 1-4`
+   sequfile="/magic/sequences/"$no"/sequence$n8.txt"
+   echo " sequence: "$sequence
+   echo " sequfile: "$sequfile
+   if ! [ "$star" = "yes" ] || [ "$cal" = "yes" ]
+   then 
+      calpath=$outpath"/callisto/$n8"
+      echo " path where calibration files are stored : "$calpath
+   fi
+   if ! [ "$cal" = "yes" ] || [ "$star" = "yes" ]
+   then 
+      starpath=$outpath"/star/$n8"
+      echo " path where star files are stored        : "$starpath
+   fi
+else
+   echo " sequfile: "$sequfile
+   if ! [ "$star" = "yes" ] || [ "$cal" = "yes" ]
+   then 
+      calpath=$outpath"/callisto"
+      echo " path where calibration files are stored : "$calpath
+   fi
+   if ! [ "$cal" = "yes" ] || [ "$star" = "yes" ]
+   then 
+      starpath=$outpath"/star"
+      echo " path where star files are stored        : "$starpath
+   fi
+fi
+
+
+if [ "$interactive" = "yes" ]
+then 
+   echo ""
+   echo "paths ok? continue?"
+   echo "please insert y, if you want continue"
+   echo "              n, if you want quit"
+
+   answer=`head -n 1`
+#   echo "answer: "$answer
+   case $answer in
+      y) echo "continue processing sequence"
+         ;;
+      n) exit
+         ;;
+      *) echo "your answer is not clear -> exit"
+         exit
+         ;;
+   esac
+fi
+
+exit
+
+
+#cd $mars
+
+if ! [ "$star" = "yes" ] || [ "$cal" = "yes" ]
+then 
+   mkdir -pv $calpath
+
+   echo "run callisto..."
+   echo "./callisto -b -q -f --log=$calpath/callisto$sequence.log --out=$calpath $sequfile "
+   ./callisto -b -q -f --log=$calpath/callisto$sequence.log --out=$calpath $sequfile 
+   check=$?
+   case $check in 
+      0)  echo "callisto finished sucessfully"
+          echo "";;
+      *)  echo -n "ERROR: callisto returned $check - please check "
+          echo -n "http://www.astro.uni-wuerzburg.de/datacenter/instructions/intern/errorcoding.txt"
+          echo " for more details"
+          exit;;
+   esac
+
+
+   calfiles=`find $calpath -name [2][0][0-2][0-9][0,1][0-9][0-3][0-9]_*_Y_*.root`
+
+   echo "run merpp update for calibrated files..."
+   echo "calibrated data files: "$calfiles
+
+   for calfile in ${calfiles[@]}
+   do
+      echo "calfile: "$calfile
+      outpath=`dirname $calfile`
+      echo "outpath: "$outpath
+
+      merpplogpath=$outpath"/merpplogs"
+      makedir $merpplogpath
+
+      runno=`echo $calfile | cut -d_ -f2 | sed -e 's/^0//' | sed -e 's/^0//' | sed -e 's/^0//' `
+      ccfile=`find /magic/subsystemdata/cc/ -name [2][0][0-2][0-9][0,1][0-9][0-3][0-9]_*${runno}_[P,D,C,S]_*_S.rep`
+      cacofile=`find /magic/subsystemdata/caco/ -name dc_[2][0][0-2][0-9]_[0,1][0-9]_[0-3][0-9]_*${runno}_*.txt`
+      echo "runno: "$runno
+      echo "ccfile: "$ccfile
+      if [ "$ccfile" = "" ]
+      then
+         echo "no ccfile found for run "$runno
+         break
+      fi
+      echo "cacofile: "$cacofile
+      if [ "$cacofile" = "" ]
+      then
+         echo "no cacofile found for run "$runno
+         echo "finding cacofile..."
+         for (( i = 0; i <= 10; i++ ))
+         do
+            newrun=`echo $runno - $i | bc`
+     #      echo "$missingcacorun + $i = $newrun"
+            path=`dirname $ccfile`
+            path=`echo $path | sed -e 's/cc/caco/'`
+            echo "path: "$path
+            cacofile=`find $path -name *$newrun*`
+            if [ "$cacofile" = "" ]
+            then
+               continue
+            else
+               break
+               echo "cacofile: "$cacofile
+            fi
+         done
+      fi
+      
+      logfile=$merpplogpath/merppccupdate$runno.log
+      echo "./merpp -u --log=$logfile --runfile=$runno $ccfile $calfile "
+      ./merpp -u --log=$logfile --runfile=$runno $ccfile $calfile
+      check=$?
+      case $check in
+         0)  ;;
+         *)  echo "ERROR: merppccupdate returned $check "
+             echo "please check the logfile $logfile "
+             exit;;
+      esac
+
+      logfile=$merpplogpath/merppcacoupdate$runno.log
+      echo "./merpp -u --log=$logfile --auto-time $cacofile $calfile "
+      ./merpp -u --log=$logfile --auto-time $cacofile $calfile
+      check=$?
+      case $check in
+         0)  ;;
+         *)  echo "ERROR: merppcacoupdate returned $check "
+             echo "please check the logfile $logfile "
+             exit;;
+      esac
+   done
+   echo "merppupdate is finished"
+   echo ""
+fi
+
+if ! [ "$cal" = "yes" ] || [ "$star" = "yes" ]
+then 
+   mkdir -pv $starpath
+
+   echo "run star..."
+   logfile=$starpath/star$sequence.log
+   if ! ls $calpath
+   then 
+      echo "couldn't find $calpath => taking standard inpath for star"
+      echo "./star -b -q -f --log=$logfile --out=$starpath $sequfile "
+      ./star -b -q -f --log=$logfile --out=$starpath $sequfile
+   else
+      echo "./star -b -q -f --log=$logfile --ind=$calpath --out=$starpath $sequfile "
+      ./star -b -q -f --log=$logfile --ind=$calpath --out=$starpath $sequfile
+   fi
+   check=$?
+   case $check in 
+      0)  echo "star finished sucessfully"
+          echo "";;
+      *)  echo "ERROR: star returned $check - please check "
+          echo "please check the logfile $logfile "
+          exit;;
+   esac
+
+   echo "star is finished "
+fi
+
+